You need to rename the files from the mod so that they match the files from the game; then the game will start reading them INSTEAD of the originals.
Regarding the griffin:
If you just want to remove the griffin without making any changes, that's one thing. But if you want to turn the griffin into a new NCF unit, or make it so that this griffin doesn't affect the original, you'll have to create a new unit with a model, animations, and other assets.
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